Basically how many nanoseconds we have to use for protein simulation? i used 20 ns for modeled structure, is it sufficient or shall i increase the time? can you suggest anyone?
For protein-Ligand simulations, duration of 20ns is sufficient. The time duration of simulations totally depends on what information you want to extract from it and to check the contribution of proteins towards your ligand binding, you can perform per-residue energy decomposition (PRED) analysis.
normally it depends on what you wanna do, for simple equilibration 20ns are sufficient, for MD run 300 ns could be good. But its totally depend on what you are looking for. BR Yogesh
As Yogesh Sonavane suggests, the length of your simulation should be problem-dependent.
I have done modelled protein-ligand simulation, so i want to know whether ligand is stable or not at that particular position. after 20 ns simulation it is binding to other amino acid residues with in the same pocket, how can i interpret this?
I feel that 20ns simulation for comprehending the protein-ligand interaction especially for studying the ligand structural rigidity is okey. But, it depends on the kind of protein you are working on, and what type of dynamics it shows?
I completely agree that 300ns simulation would be nice, but it is beyond expectation when you have simple workstation and protein system of 70-80k atoms.
Now, ur query regarding the results interpretation, you can simply identify the residue interactions, RMSD, fluctuations in the H-bonds and lots more in the trajectory file generated in the MD.
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